Quasi-prime peptides: identification of the shortest peptide sequences unique to a species.
Quasi-prime peptides: identification of the shortest peptide sequences unique to a species.
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DOI：
10.1093/nargab/lqad039
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发表时间：
2023-06
影响因子：
4.6
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中科院分区：
文献类型：
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确定生物样本中存在的生物体在农业、野生动物保护和医疗保健中有许多重要的应用。在这里，我们开发了一种通用的指纹图谱，基于对特定生物体特有的短肽的识别。我们将准素肽定义为只在一个物种中发现的序列，我们分析了从病毒到人类的21到875个物种的蛋白质组，并注释了一个物种特有的最小的肽kmer序列，这些序列在所有其他蛋白质组中都没有。我们还对所有参考蛋白质组进行模拟，并观察到跨物种和分类的肽kmer数量低于预期，这表明空肽丰富，即蛋白质组中不存在的序列。对于人类，我们发现在富含特定基因本体论术语的基因中发现了准素，包括蛋白酶体、ATP和GTP催化。我们还为一些人类病原体和模式生物提供了一套准素肽，并通过结核分枝杆菌和霍乱弧菌的两个案例研究进一步展示了它的有效性，在这两个案例中，我们识别了两个与病原体检测相关的跨膜和细胞外蛋白中的准素肽。我们的准质肽目录提供了蛋白质水平上特定于单个生物体的最小单位的信息，为物种鉴定提供了一个通用的工具。
Determining the organisms present in a biosample has many important applications in agriculture, wildlife conservation, and healthcare. Here, we develop a universal fingerprint based on the identification of short peptides that are unique to a specific organism. We define quasi-prime peptides as sequences that are found in only one species, and we analyzed proteomes from 21 875 species, from viruses to humans, and annotated the smallest peptide kmer sequences that are unique to a species and absent from all other proteomes. We also perform simulations across all reference proteomes and observe a lower than expected number of peptide kmers across species and taxonomies, indicating an enrichment for nullpeptides, sequences absent from a proteome. For humans, we find that quasi-primes are found in genes enriched for specific gene ontology terms, including proteasome and ATP and GTP catalysis. We also provide a set of quasi-prime peptides for a number of human pathogens and model organisms and further showcase its utility via two case studies for Mycobacterium tuberculosis and Vibrio cholerae, where we identify quasi-prime peptides in two transmembrane and extracellular proteins with relevance for pathogen detection. Our catalog of quasi-prime peptides provides the smallest unit of information that is specific to a single organism at the protein level, providing a versatile tool for species identification.